Velvet Preferences

Velvet

Velvet is a de novo assembler intended for next generation reads.

Reads pre-processing

Discard short reads that contain any N?s (default on)

By default any short reads with N's are removed from the analysis.

Trim ends with quality less than (default 20)

If the ends of reads have low quality then they are trimmed before being assembled.

Long reads are at least X nt (default 250)

Velvet treats long reads and short reads differently. This defines at which length a read is judged to be a long read.

Initial velveth Processing

Before being assembled by Velvethg, Velveth is used to process the reads.

Hash ("K-MER") Length (default 39)

This is the "word" length that will be used to build the de Brujinn graph in the second step of assembly by VelvetG. This must be an odd number and must be less than the length of the reads.

Source files contain paired reads (default no)

Auto (default no)

Short Read insert length (-ins_length, default 400)

Long Read insert length (-ins_length, default 10,000)

This is used for paired reads (ignored otherwise) and is the length of the insert, INCLUDING reads, that was sequenced. It can be automatically determined by VELVETG if the reads are of a consistent lengths so Auto is the best default option I think.

Override automatic coverage defaults (default off)

Coverage cutoff (-cov_cutoff, default 5) Auto (default no)

Below a certain coverage reads are not assembled into contigs and are ignored. This can also be automatically determined.

Expected coverage (-exp_cov, default 50) Auto (no)

This is the expected average coverage. If it is consistent over the entire assembly AUTO can be used.

Min contig length (-mincontiglgth, default 500)

This is to reduce noise from many small contigs in the results. It does not affect the statistics but filters out contigs below a certain size. For example with the default value only contigs of 500bp or longer are shown.

Maximum coverage (-max_coverage, default 500)

This is the highest coverage expected. This should help with repeats as the algorithm will know that peaks with coverage over this limit are likely repeats.

Advanced parameters

Disable scaffolding (-scaffolding, default no)

By default Velvet will insert a series of N's between each read in a pair where the sequence of the insert between the pair is unknown although the insert is of a known length.

min. pair count (-minpaircount, default 5, range of values 1 - 20)

Minimum number of paired end connections to justify the scaffolding of two long contigs.

Max. branch gaps (-maxgapcount, default 3, range of values 0-10)

Maximum number of gaps allowed in the alignment of the two branches of a bubble.

Long Read merge cutoff (-longmultcutoff, default 2, range of values 0 - 20)

Minimum number of long reads required to merge contigs.

Max. branch length (-maxbranchlength, default 100)

Maximum length in base pairs of a bubble produced by mismatches in a contig.

Max. branch divergence (-max_divergence, default 0.2, range of values 0.0 - 1.0)

Maximum divergence rate between two branches in a bubble.

For more details on using Velvet see the Velvet technical page